Variant report

Variant	rs1001581
Chromosome Location	chr19:44065388-44065389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr19:44065282-44065632	K562	blood:	n/a	n/a
2	TAL1	chr19:44065282-44065622	K562	blood:	n/a	chr19:44065443-44065461

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44065179..44067890-chr19:44122794..44124973,2	K562	blood:
2	chr19:44063536..44067996-chr19:44097389..44100718,5	MCF-7	breast:

Variant related genes	Relation type
XRCC1	TF binding region
ENSG00000167378	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000131116	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12611088	0.86[EUR][1000 genomes]
rs1799778	0.92[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs2256507	0.92[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs25486	0.92[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs25487	0.92[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs2599465	0.84[EUR][1000 genomes]
rs2682559	0.85[EUR][1000 genomes]
rs3810378	0.81[CEU][hapmap];0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1063149	chr19:44059081-44087583	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1001581	SLC8A2	cis	cerebellum	SCAN
rs1001581	TRPM4	cis	cerebellum	SCAN
rs1001581	SLC17A7	cis	cerebellum	SCAN
rs1001581	BCAT2	cis	cerebellum	SCAN
rs1001581	CD37	cis	parietal	SCAN
rs1001581	ZNF649	cis	parietal	SCAN
rs1001581	BCAT2	cis	parietal	SCAN
rs1001581	IL4I1	cis	cerebellum	SCAN
rs1001581	TEAD2	cis	parietal	SCAN
rs1001581	IZUMO1	cis	cerebellum	SCAN
rs1001581	ZNF575	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44039200-44078600	Weak transcription	Hela-S3	cervix
2	chr19:44043600-44065800	Strong transcription	Adipose Nuclei	Adipose
3	chr19:44043800-44065800	Weak transcription	Fetal Heart	heart
4	chr19:44043800-44074000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:44044600-44069000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:44047400-44066600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:44048200-44067000	Weak transcription	HUVEC	blood vessel
8	chr19:44048400-44078800	Weak transcription	Small Intestine	intestine
9	chr19:44052800-44068400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:44053000-44065600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr19:44053000-44066200	Strong transcription	Fetal Muscle Leg	muscle
12	chr19:44053400-44068800	Strong transcription	Fetal Intestine Small	intestine
13	chr19:44053400-44069400	Strong transcription	Fetal Stomach	stomach
14	chr19:44053600-44068600	Strong transcription	Fetal Intestine Large	intestine
15	chr19:44054000-44065600	Strong transcription	Placenta	Placenta
16	chr19:44056000-44066600	Weak transcription	Psoas Muscle	Psoas
17	chr19:44056400-44066400	Weak transcription	Stomach Mucosa	stomach
18	chr19:44057200-44067000	Weak transcription	Fetal Brain Male	brain
19	chr19:44057600-44071200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr19:44057800-44078800	Weak transcription	HSMMtube	muscle
21	chr19:44058400-44071400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr19:44058600-44078800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr19:44059000-44076000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:44059200-44066600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr19:44059200-44066800	Weak transcription	HMEC	breast
26	chr19:44059200-44078800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr19:44059400-44066600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:44059800-44066600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr19:44059800-44078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr19:44060400-44065800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr19:44060400-44066600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:44061600-44065400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr19:44061800-44069000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:44062400-44066400	Weak transcription	Colon Smooth Muscle	Colon
35	chr19:44062400-44067400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:44062400-44067400	Strong transcription	Fetal Brain Female	brain
37	chr19:44062600-44066600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:44062600-44076000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:44062800-44066400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr19:44063200-44066800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:44063400-44065400	Strong transcription	Brain Anterior Caudate	brain
42	chr19:44063400-44067400	Strong transcription	Brain Germinal Matrix	brain
43	chr19:44063400-44076200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:44063600-44065800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:44063600-44065800	Strong transcription	Liver	Liver
46	chr19:44063600-44069200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:44063800-44065400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:44063800-44065400	Strong transcription	Dnd41	blood
49	chr19:44063800-44066200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr19:44063800-44066400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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